Agent-Skills.md

Agent Skills: GROMACS Biosim Runner Skill

GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations

physicsID: a5c-ai/babysitter/gromacs-biosim-runner

Repository

a5c-ai/babysitter
a5c-aiLicense: MIT
244

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pnpm dlx add-skill https://github.com/a5c-ai/babysitter/tree/HEAD/plugins/babysitter/skills/babysit/process/specializations/domains/science/physics/skills/gromacs-biosim-runner

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plugins/babysitter/skills/babysit/process/specializations/domains/science/physics/skills/gromacs-biosim-runner/SKILL.md

Skill Metadata

Name
gromacs-biosim-runner
Description
GROMACS molecular dynamics skill specialized for biomolecular systems, protein simulations, and free energy calculations

GROMACS Biosim Runner Skill

Purpose

Provide specialized integration with GROMACS for biomolecular simulations including protein dynamics, free energy calculations, and enhanced sampling methods.

Capabilities

  • Topology preparation and solvation
  • Energy minimization workflows
  • NPT/NVT equilibration protocols
  • Free energy perturbation setup
  • Trajectory analysis (RMSD, RMSF, RDF)
  • Enhanced sampling methods (metadynamics, replica exchange)

Usage Guidelines

  • Use appropriate water models (TIP3P, TIP4P, SPC/E)
  • Select force fields compatible with target biomolecules (AMBER, CHARMM, OPLS)
  • Follow standard equilibration protocols
  • Monitor system stability during production runs

Dependencies

  • GROMACS
  • pdb2gmx
  • MDAnalysis
  • PLUMED (for enhanced sampling)

Process Integration

  • Molecular Dynamics Simulation Setup
  • High-Performance Computing Workflow